The oligosaccharides of the Fe(III)‐Zn(II) purple acid phosphatase of the red kidney bean: Determination of the structure by a combination of matrix‐assisted laser desorption/ionization mass spectrometry and selective enzymic degradation

Purple acid phosphatase of the common bean Phaseolus vulgaris (KBPase), a dimeric 110‐kDa glycoprotein related to the mammalian purple acid phosphatases with a two‐metal cluster at the active site contains five oligosaccharide side chains/monomer. The N‐linked glycan structures were characterized by selective enzymic degradation in combination with matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). The purified protein was cleaved by cyanogen bromide. One 30‐kDa large methionine‐free fragment required a further tryptic digest. The peptides were separated by HPLC and the glycosylated species were identified both by their heterogeneous mass spectra and by an immunoassay. None of the glycopeptides proved to have more than one glycosylation site. The composition of the carbohydrate moieties were calculated by comparing the mass spectra of the glycopeptides before and after enzymic deglycosylation. These results were complemented by data from a carbohydrate composition analysis. In four of the five peptides an α1–3 fucose attached to the asparagine‐linked N‐acetylglucosamine prevented removal of the glycan by peptide N‐glycosidase F; peptide N‐glycosidase A removed all carbohydrates from the peptides. To reveal the sequence of the carbohydrate moiety including the linkage positions between the different saccharides, one of the glycopeptides was degraded by specific exoglycosidases. The enzymic degradations by these hydrolases were monitored by mass spectrometry of small aliquots taken at intervals during the reaction. The detailed structure of this one glycan in conjunction with the respective mass spectra and the composition analysis were used to infer the structure of the other four glycans. All glycans of the KBPase have a complex‐type xylose‐containing structure with four of the five having an additional fucose.